dynamo.pl.fate

dynamo.pl.fate(adata, x=0, y=1, basis='pca', color='ntr', ax=None, save_show_or_return='show', save_kwargs={}, **kwargs)[source]

Draw the predicted integration paths on the low-dimensional embedding.

Parameters

  • adata (AnnData) – an Annodata object

  • basis (str) – The reduced dimension.

  • x (int (default: 0)) – The column index of the low dimensional embedding for the x-axis.

  • y (int (default: 1)) – The column index of the low dimensional embedding for the y-axis.

  • color (string (default: ntr)) – Any column names or gene expression, etc. that will be used for coloring cells.

  • ax (matplotlib.Axis (optional, default None)) – The matplotlib axes object where new plots will be added to. Only applicable to drawing a single component.

  • save_show_or_return (str {‘save’, ‘show’, ‘return’} (default: show)) – Whether to save, show or return the figure. If “both”, it will save and plot the figure at the same time. If “all”, the figure will be saved, displayed and the associated axis and other object will be return.

  • save_kwargs (dict (default: {})) – A dictionary that will passed to the save_fig function. By default it is an empty dictionary and the save_fig function will use the {“path”: None, “prefix”: ‘scatter’, “dpi”: None, “ext”: ‘pdf’, “transparent”: True, “close”: True, “verbose”: True} as its parameters. Otherwise you can provide a dictionary that properly modify those keys according to your needs.

  • kwargs (dict) – Additional arguments passed to pl.scatters or plt.scatters.

Returns

Either None or a matplotlib axis with the relevant plot displayed. If you are using a notbooks and have %matplotlib inline set then this will simply display inline.

Return type

result